The target information is not stored in the registration file, so you have to specify it on the command-line of mri_vol2vol. I don't know what your command line was, but you have to specify a mov and a targ and a reg. Information about the reoriented space is basically stored in a combination of the reg file and the geometry in the target volume.
doug Bruce Fischl wrote: > Hi Timour > > I'll leave 1) to Doug. As for 2), the aseg.mgz is an index map into the > FreeSurferColorLUT.txt (e.g. voxel value 17 means Left Hippocampus), so > nearest nbr interpolation is the only kind that makes sense. Otherwise you > will average index value which will give you a useless image. > > cheers > Bruce > > > > On Tue, 9 Nov 2010, Timour Al-Khindi wrote: > > >> Hello, >> >> We are looking for a way to reorient the orig.mgz files and the segmentation >> (aseg.mgz) into a different plane, and we have a couple of questions. We've >> used tkregister2 to reorient the orig image: >> >> tkregister2 ?mov orig.mgz ?tar orig.mgz ?regheader ?reg myregister.dat >> >> myregister.dat is created by this command line. We rotate the brain in the >> tkregister2 gui, then save the registration. Finally, we use the mri_vol2vol >> command line to rotate the orig and the aseg images. >> >> For aseg.mgz: >> mri_vol2vol --mov aseg.mgz --targ orig.mgz --reg myregister.dat --interp >> nearest --o rotaseg.mgz >> >> For orig.mgz: >> mri_vol2vol --mov orig.mgz --targ aseg.mgz --reg myregister.dat --o >> rotorig.mgz >> >> This seems to look decent when we load it up in tkmedit, but we have two >> questions about the use of mri_vol2vol >> >> 1) Why does the algorithm need a target (won't run without it), since the >> transformation info is saved in myregister.dat? Also, how does it manage to >> work (which it does), given than neither of the targets entered are in the >> reoriented space? Should we use a different target? What is the role of the >> target? >> >> 2) A previous post specifies that "interp nearest" should be used to rotate >> the aseg.mgz file. What is the function played by that command? Should we >> also use it when rotating the orig.mgz file? It works without it, but do we >> risk distorting the image? >> >> Thanks in advance! >> >> Tim Al-Khindi >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
